pro spectrum_flag

;read the fits file into an array of IDL structures. You can replace this file name with
;any of the Greenbank sdfits files.
arr=mrdfits('1422_200MHz.raw.acs.fits',1,header)

;get the number of rows in this array
dims = size(arr, /dimensions)
numRows = dims[0] ; number of rows (spectra)

;get the number of channels.
channels=size(arr[0].data,/n_elements)

;define an array that will hold all the spectra of one Stokes parameter
;since there are 4 Stokes and each integration has a calon and caloff, we
;must skip 8 rows each time (see loop below).
image=fltarr(channels,numRows/8.)

;here we are fitting a 10th order polynomial to the first spectrum, normalizing it,
;then dividing each spectrum by this to flatten it (called bandpass calibration).
;looks like we may need to go hire than 10th order. I'll keep it commented out for now.
;x=findgen(4096)  ;a fake channel axis just for doing the fit
;spec=arr[0].data ;getting the first spectra in the array
;fit=polyfit(x,spec,10) ;fitting a 10th order polynomial to the data
;creating a baseline vecter and normalizing it
;baseline=fit[0]+fit[1]*x+fit[2]*(x)^2+fit[3]*(x)^3+fit[4]*(x)^4+fit[5]*(x)^5+fit[6]*(x)^6+fit[7]*(x)^7+fit[8]*(x)^8+fit[9]*(x)^9+fit[10]*(x)^10
;basen=baseline/max(baseline)

;looping through very 8th spectrum and putting it into a row of the array 'image'. Once we add in the baseline calibration
;we will divide by 'basen' from the above polynomial fit.
for i=0,numRows-8,8 do begin
image[*,i/8.]=arr[i].data
endfor

;Here we write the image into a fits file and open it with my program 'fitsview.pro', which is a very basic GUI for looking at
;fits files.
writefits, 'spectral_flag_baseline.fits',image
fitsview,'spectral_flag_baseline.fits'
end